pre-submit formater

Author: YihanWangAstro

.clang-format

@@ -0,0 +1,72 @@
+---
+# Based on LLVM style with modifications for your codebase
+BasedOnStyle: LLVM
+
+# Basic formatting
+IndentWidth: 4
+TabWidth: 4
+UseTab: Never
+ColumnLimit: 120
+
+# Brace wrapping
+BreakBeforeBraces: Attach
+Cpp11BracedListStyle: true
+
+# Indentation
+IndentCaseLabels: true
+IndentPPDirectives: BeforeHash
+AccessModifierOffset: -2
+
+# Alignment
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignOperands: true
+AlignTrailingComments: true
+
+# Spacing
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+
+# Line breaks
+AllowShortBlocksOnASingleLine: Empty
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+
+# Includes
+SortIncludes: true
+IncludeBlocks: Regroup
+IncludeCategories:
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*>'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+
+# Pointers and references
+DerivePointerAlignment: false
+PointerAlignment: Left
+
+# Comments (preserve your existing comment style)
+ReflowComments: false
+
+# Constructor initializers
+BreakConstructorInitializers: BeforeColon
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+
+# Template arguments
+AlwaysBreakTemplateDeclarations: Yes
+
+# Namespace
+NamespaceIndentation: All

.github/workflows/PyPI-build.yml

@@ -27,7 +27,7 @@ jobs:
           python -m pip install cibuildwheel
           python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: "cp38-* cp39-* cp310-* cp311-* cp312-* cp313-*" 
+          CIBW_BUILD: "cp38-* cp39-* cp310-* cp311-* cp312-* cp313-*"
           CIBW_SKIP: "*-win32* *_i686* *musllinux*"
           CIBW_ARCHS_WINDOWS: "AMD64 ARM64"
           CIBW_ARCHS_MACOS: "x86_64 arm64"
@@ -47,7 +47,7 @@ jobs:
     needs: build_wheels
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/v')
-    
+
     steps:
       - uses: actions/checkout@v4
 
@@ -76,4 +76,4 @@ jobs:
         with:
           package_dir: dist
           user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/docs.yml

@@ -15,23 +15,23 @@ on:
 jobs:
   build_and_deploy:
     runs-on: ubuntu-latest
-    
+
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-          
+
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
           python-version: '3.9'
-          
+
       - name: Install Doxygen
         run: |
           sudo apt-get update
           sudo apt-get install -y doxygen graphviz
-          
+
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
@@ -42,64 +42,64 @@ jobs:
           cd docs
           chmod +x build_docs.sh
           ./build_docs.sh
-          
+
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
         with:
           personal_token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
           publish_dir: ./docs/build/html
           destination_dir: docs
-          
+
       - name: Create Wiki Content
         run: |
           # Install pandoc for HTML to Markdown conversion
           sudo apt-get install -y pandoc
-          
+
           # Create a directory for wiki content
           mkdir -p wiki_content
-          
+
           # Copy Home.md with proper formatting
           cat > wiki_content/Home.md << 'EOL'
           # VegasAfterglow Documentation
-          
+
           Welcome to the VegasAfterglow documentation wiki.
-          
+
           ## Documentation
-          
+
           The complete documentation is published to GitHub Pages. Please visit:
-          
+
           **[Full Documentation Site](https://yihanwangastro.github.io/VegasAfterglow/docs/)**
-          
+
           ## Quick Links
-          
+
           * [C++ API Reference](https://yihanwangastro.github.io/VegasAfterglow/docs/cpp_api.html)
           * [Python API Reference](https://yihanwangastro.github.io/VegasAfterglow/docs/python_api.html)
           * [Installation Guide](https://yihanwangastro.github.io/VegasAfterglow/docs/installation.html)
           * [Quick Start Guide](https://yihanwangastro.github.io/VegasAfterglow/docs/quickstart.html)
           * [Examples](https://yihanwangastro.github.io/VegasAfterglow/docs/examples.html)
           * [Contributing Guide](https://yihanwangastro.github.io/VegasAfterglow/docs/contributing.html)
-          
+
           ## Building Documentation Locally
-          
+
           To build the documentation locally, please refer to the [docs/README.md](https://github.com/YihanWangAstro/VegasAfterglow/blob/main/docs/README.md) file in the main repository.
           EOL
-          
+
           # Create sidebar navigation
           cat > wiki_content/_Sidebar.md << 'EOL'
           ## VegasAfterglow
-          
+
           * [Home](Home)
           * [Documentation Site](https://yihanwangastro.github.io/VegasAfterglow/docs/)
           EOL
-          
+
           # Create footer
           cat > wiki_content/_Footer.md << 'EOL'
           ---
           Documentation generated automatically from the [VegasAfterglow repository](https://github.com/YihanWangAstro/VegasAfterglow).
           EOL
-      
+
       - name: Push to Wiki
         uses: Andrew-Chen-Wang/github-wiki-action@v4
         with:
           path: wiki_content
-          token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }} 
+          token: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}

.gitignore

@@ -0,0 +1,25 @@
+**/*.txt
+**/*.csv
+**/*.dat
+**/*.out
+**/*.log
+**/*.err
+**/*.warn
+**/*.a
+**/*.so
+**/*.npy
+**/*.npz
+**/.DS_Store
+**/*.pyc
+
+external/
+projects/
+build/
+.vscode/
+.idea/
+.DS_Store
+vegasglow.so.dSYM/
+!CMakeLists.txt
+
+docs/build/
+docs/doxygen/

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+repos:
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.12.1
+    hooks:
+      - id: black
+        language_version: python3
+        files: ^VegasAfterglow/.*\.py$
+
+  # Python import sorting
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        files: ^VegasAfterglow/.*\.py$
+
+  # Python linting
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        args: ["--max-line-length=88", "--extend-ignore=E203,W503"]
+        files: ^VegasAfterglow/.*\.py$
+
+  # C++ formatting
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v17.0.6
+    hooks:
+      - id: clang-format
+        files: \.(cpp|hpp|c|h|cc|cxx)$
+        exclude: ^external/.*
+
+  # General file cleanup
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: ^external/.*
+      - id: end-of-file-fixer
+        exclude: ^external/.*
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+
+  # Check for common issues
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-case-conflict
+      - id: mixed-line-ending
+        args: ['--fix=lf']
+        exclude: ^external/.*

CHANGELOG.md

@@ -54,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **StepPowerLawJet**: New jet model with parameters `(theta_c, E_iso_c, Gamma0_c, E_iso_w, Gamma0_w, k_e, k_g)`
 - **Wind Medium**: Extended with optional `n_ism` and `n_0` parameters for stratified medium modeling: `Wind(A_star, n_ism=0, n_0=inf)`
 - **Medium Class**: Simplified from `Medium(rho, mass)` to `Medium(rho)` - removed separate mass parameter
-- **Model Methods**: 
+- **Model Methods**:
   - Removed `specific_flux_sorted_series()` method
   - Added `specific_flux_series_with_expo(t, nu, expo_time, num_points=10)` for exposure time averaging
   - Changed `details(t_obs)` to `details(t_min, t_max)` interface
@@ -340,4 +340,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ---
 
 For detailed information about each release, see the individual version sections above.
-For the latest updates and development progress, visit our [GitHub repository](https://github.com/YihanWangAstro/VegasAfterglow).
+For the latest updates and development progress, visit our [GitHub repository](https://github.com/YihanWangAstro/VegasAfterglow).

CMakeLists.txt

@@ -43,4 +43,4 @@ if(NOT CMAKE_BUILD_TYPE)
 endif()
 
 # Install the module into the Python package directory
-install(TARGETS VegasAfterglowC DESTINATION VegasAfterglow)
+install(TARGETS VegasAfterglowC DESTINATION VegasAfterglow)

LICENSE

@@ -26,4 +26,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Makefile

@@ -54,4 +54,4 @@ info:
 	@echo "Platform: $(PLATFORM)"
 	@echo "Compiler: $(CXX)"
 	@echo "CXXFLAGS: $(CXXFLAGS)"
-	@echo "LDFLAGS: $(LDFLAGS)"
+	@echo "LDFLAGS: $(LDFLAGS)"